This engine has been out there for a couple years despite the 2012 introduction to the JK Wrangler, are there any initial issues connected to this power train? What is the overall consensus? Any specific items to keep an eye on?

Here are a few links talking about the 3.6 Pentastar. As you can see in the third link though, you can't judge reliability simply on the basis of length of time on the market as the motor is tuned differently for different applications.

Unfortunately I can't give any first hand information on the engine as mine has the 3.8.

ironic that it hasn't done it since i posted that.
approaching 7,000 miles. no further issue out of the engine. i'm very happy with it and would trust buying another one. its a power house in the heavy Journey.

My worries are based in that I typically choose to purchase vehicles once they are proven rather than taking my chances of getting something with major inherent problems (think of the Cadillac 4.1L and wasn't it Chrysler that had the 3.0 that was terrible a decade ago?). I really miss the straight six that Jeeps had for so many years.